We have studied the influence of different annealing conditions on refractive index profiles of He and H ions implanted lithium niobate planar waveguides. After annealing treatment with different times and different temperatures the dark modes of both kinds of waveguides are measured by using a prism coupling method. The refractive index profiles of both waveguides before and after annealing treatment are given. The results show that both He and H ions implantations result in the decrease of the ordinary refractive index in barriers, but in the region of guides the extraordinary refractive index increases. Annealing treatment influences the ordinary refractive index profiles obviously, but under 400°C the annealing treatment alomost has no influence on the extraordinary refractive index profiles.